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High-performance computing and molecular dynamics

Grant number: 21/03224-3
Support Opportunities:Scholarships in Brazil - Post-Doctorate
Effective date (Start): June 01, 2021
Effective date (End): May 31, 2024
Field of knowledge:Physical Sciences and Mathematics - Computer Science - Computer Systems
Principal Investigator:Guido Costa Souza de Araújo
Grantee:Oscar Samuel Cajahuaringa Macollunco
Host Institution: Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
Associated research grant:13/08293-7 - CCES - Center for Computational Engineering and Sciences, AP.CEPID


Mass spectrometry is a vital tool for molecular characterization in many areas of Biochemistry analysis. Ion-Mobility Mass Spectrometry (IM-MS) CCS is an analytical (experimental) technique used to separate and identify ionized molecules moving through a drifting gas based on their mobility. In such experiments, molecules can move in a tube and bump into gas molecules. As a result, gas molecules are reflected and the combination of the resulting collision angles is used to estimate the molecule Collision Cross Section (CCS) which depends on the molecule structure. CCS can have a number of applications like determine the conformation of molecules. It can also be used to answer a number of relevant research questions like: (a) What is the real range and flexibility of cross-linkers bound to proteins?; (b) Are proteins really stable in gas phase?; and (c) What is the charge density distribution in IM-MS conditions? Mobcal is a well- known software for CCS computation. Our group at IC-UNICAMP has worked closely with members of CCES and the Chemistry Institute of UNICAMP to improve the performance of Mobcal simulation. The complexity of the simulation grows considerably high as we increase the size of the molecule. We have parallelized CCS simulation in Mobcal using OpenMP and MPI and tested it using a number of molecules from small Ubiquitin (1201 atoms) to larger polypeptide molecule (such as 5leg constituted by 18694 atoms). The results show that our approach can considerably reduce the CCS computation time. We are planning to extend Mobcal simulation with Linked-cell techniques to improve simulation speed-up, thus enabling the CCS computation of large proteins. The PD scholarship associated to this submission will initially focus in performing this extension using the OpenMP Cluster parallel programming model developed at IC-UNICAMP. This is joint collaboration with the Computing and Chemistry Institutes of UNICAMP. (AU)

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